LAMMPS (4 Nov 2022)
# 20 styrene molecules
# three reactions defined

units real

boundary p p p

atom_style full

kspace_style pppm 1.0e-4

pair_style lj/class2/coul/long 8.5

angle_style class2

bond_style class2

dihedral_style class2

improper_style class2

variable T equal 530

read_data tiny_polystyrene.data    extra/bond/per/atom 5   extra/angle/per/atom 15   extra/dihedral/per/atom 15   extra/improper/per/atom 25   extra/special/per/atom 25
Reading data file ...
  orthogonal box = (1.7426663 1.7426663 1.7426663) to (18.257334 18.257334 18.257334)
  1 by 1 by 1 MPI processor grid
  reading atom labelmap ...
  reading bond labelmap ...
  reading angle labelmap ...
  reading dihedral labelmap ...
  reading improper labelmap ...
  reading atoms ...
  320 atoms
  reading velocities ...
  320 velocities
  scanning bonds ...
  8 = max bonds/atom
  scanning angles ...
  18 = max angles/atom
  scanning dihedrals ...
  22 = max dihedrals/atom
  scanning impropers ...
  26 = max impropers/atom
  reading bonds ...
  320 bonds
  reading angles ...
  480 angles
  reading dihedrals ...
  640 dihedrals
  reading impropers ...
  160 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     3 = max # of 1-2 neighbors
     6 = max # of 1-3 neighbors
    12 = max # of 1-4 neighbors
    39 = max # of special neighbors
  special bonds CPU = 0.001 seconds
  read_data CPU = 0.015 seconds

molecule mol1 2styrene_unreacted.molecule_template
Read molecule template mol1:
  1 molecules
  0 fragments
  32 atoms with max type 4
  32 bonds with max type 11
  48 angles with max type 19
  64 dihedrals with max type 21
  16 impropers with max type 8
molecule mol2 2styrene_reacted.molecule_template
Read molecule template mol2:
  1 molecules
  0 fragments
  32 atoms with max type 6
  33 bonds with max type 13
  54 angles with max type 22
  79 dihedrals with max type 19
  14 impropers with max type 7
molecule mol3 chain_plus_styrene_unreacted.molecule_template
Read molecule template mol3:
  1 molecules
  0 fragments
  46 atoms with max type 6
  47 bonds with max type 13
  75 angles with max type 22
  105 dihedrals with max type 21
  21 impropers with max type 8
molecule mol4 chain_plus_styrene_reacted.molecule_template
Read molecule template mol4:
  1 molecules
  0 fragments
  46 atoms with max type 6
  48 bonds with max type 13
  81 angles with max type 22
  121 dihedrals with max type 19
  19 impropers with max type 7
molecule mol5 chain_chain_unreacted.molecule_template
Read molecule template mol5:
  1 molecules
  0 fragments
  50 atoms with max type 6
  51 bonds with max type 13
  84 angles with max type 22
  118 dihedrals with max type 19
  20 impropers with max type 7
molecule mol6 chain_chain_reacted.molecule_template
Read molecule template mol6:
  1 molecules
  0 fragments
  50 atoms with max type 6
  52 bonds with max type 13
  90 angles with max type 22
  135 dihedrals with max type 19
  18 impropers with max type 2

thermo 100

# dump 1 all xyz 5 test_vis.xyz

fix rxn1 all bond/react stabilization yes statted_grp .03  react rxn1 all 1 0 3.0 mol1 mol2 2styrene_map stabilize_steps 100  react rxn2 all 1 0 3.0 mol3 mol4 chain_plus_styrene_map stabilize_steps 100  react rxn3 all 1 0 5.0 mol5 mol6 chain_chain_map stabilize_steps 100
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined

fix 1 statted_grp_REACT nvt temp $T $T 100
fix 1 statted_grp_REACT nvt temp 530 $T 100
fix 1 statted_grp_REACT nvt temp 530 530 100

fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
fix 4 bond_react_MASTER_group temp/rescale 1 530 $T 1 1
fix 4 bond_react_MASTER_group temp/rescale 1 530 530 1 1

thermo_style custom step temp press density f_rxn1[1] f_rxn1[2] f_rxn1[3]

run 10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012

@Article{Gissinger17,
 author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
 title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
 journal = {Polymer},
 year =    2017,
 volume =  128,
 pages =   {211--217}
}

@Article{Gissinger20,
 author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
 title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
 journal = {Macromolecules},
 year =    2020,
 volume =  53,
 number =  22,
 pages =   {9953--9961}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.004 (../kspace.cpp:327)
  using 12-bit tables for long-range coulomb (../kspace.cpp:342)
  G vector (1/distance) = 0.25561147
  grid = 6 6 6
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0097469157
  estimated relative force accuracy = 2.9352547e-05
  using double precision KISS FFT
  3d grid and FFT values/proc = 1331 216
Generated 21 of 21 mixed pair_coeff terms from sixthpower/geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10.5
  ghost atom cutoff = 10.5
  binsize = 5.25, bins = 4 4 4
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) pair lj/class2/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
  (2) fix bond/react, occasional, copy from (1)
      attributes: half, newton on
      pair build: copy
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 31.51 | 31.51 | 31.51 Mbytes
   Step          Temp          Press         Density       f_rxn1[1]      f_rxn1[2]      f_rxn1[3]   
         0   320.13638     -376.0844       0.76796752     0              0              0            
       100   342.22237     -3489.4495      0.76796752     0              0              0            
       200   412.23828     -1367.104       0.76796752     0              0              0            
       300   467.98145      4841.002       0.76796752     0              0              0            
       400   505.39864      2213.0509      0.76796752     1              0              0            
       500   519.63371     -28223.513      0.76796752     2              0              0            
       600   526.40655      8701.2728      0.76796752     2              0              0            
       700   579.91953      2507.5868      0.76796752     2              0              0            
       800   517.29593      5558.2894      0.76796752     2              0              0            
       900   503.38392     -5027.1155      0.76796752     2              0              0            
      1000   509.30766      3979.0526      0.76796752     2              0              0            
      1100   551.34763      5119.0854      0.76796752     2              0              0            
      1200   562.51766     -2867.8721      0.76796752     2              0              0            
      1300   552.90947      2090.7196      0.76796752     2              0              0            
      1400   516.10667      3374.3471      0.76796752     2              0              0            
      1500   518.70363      472.0237       0.76796752     2              0              0            
      1600   559.50145      5451.1908      0.76796752     2              0              0            
      1700   531.49515      4526.9547      0.76796752     2              0              0            
      1800   529.18545     -3566.8838      0.76796752     2              0              0            
      1900   517.52577     -2390.6662      0.76796752     2              0              0            
      2000   495.24246     -485.62368      0.76796752     2              0              0            
      2100   567.90338      2009.3507      0.76796752     3              0              0            
      2200   553.05006      5694.0307      0.76796752     3              0              0            
      2300   561.22521      2944.2766      0.76796752     3              0              0            
      2400   460.05535      3058.3944      0.76796752     3              0              0            
      2500   501.01426      365.04418      0.76796752     4              0              0            
      2600   543.94728      267.33298      0.76796752     4              0              0            
      2700   539.40536      4258.9345      0.76796752     4              0              0            
      2800   557.67853     -2732.3135      0.76796752     4              0              0            
      2900   539.85456      3987.7331      0.76796752     4              1              0            
      3000   501.3125       3280.3821      0.76796752     4              1              0            
      3100   537.77092     -5290.371       0.76796752     4              1              0            
      3200   528.20744      11690.902      0.76796752     4              1              0            
      3300   548.56721      2464.6039      0.76796752     4              1              0            
      3400   542.73725     -27951.173      0.76796752     4              1              1            
      3500   547.63988      7925.1202      0.76796752     4              1              1            
      3600   502.69726      7875.8308      0.76796752     4              1              1            
      3700   495.26614     -1907.7215      0.76796752     4              1              1            
      3800   526.91826     -4267.1784      0.76796752     4              1              1            
      3900   538.8248       6811.7446      0.76796752     4              1              1            
      4000   531.42158      5031.2992      0.76796752     4              1              1            
      4100   539.69772      6278.9861      0.76796752     4              1              1            
      4200   519.11497      9206.6513      0.76796752     4              1              1            
      4300   518.08237     -63.769046      0.76796752     4              1              1            
      4400   582.43352      4189.0234      0.76796752     4              1              1            
      4500   541.87979     -2072.4133      0.76796752     4              1              1            
      4600   514.7508       7502.1057      0.76796752     4              1              1            
      4700   530.22173      51.50674       0.76796752     4              1              1            
      4800   507.14885      5148.7797      0.76796752     4              1              1            
      4900   516.05055      9110.3072      0.76796752     4              1              1            
      5000   552.55865      7310.0399      0.76796752     4              1              1            
      5100   581.79588      3282.8939      0.76796752     4              1              1            
      5200   523.07607     -1312.6111      0.76796752     4              1              1            
      5300   528.44235     -2242.0268      0.76796752     4              1              1            
      5400   537.63408      4599.5474      0.76796752     4              1              1            
      5500   526.75093      5551.7841      0.76796752     4              1              1            
      5600   562.74766      2764.4556      0.76796752     4              1              1            
      5700   545.12259     -3139.3468      0.76796752     4              1              1            
      5800   563.77404      4261.7786      0.76796752     4              1              1            
      5900   514.07804      4057.43        0.76796752     4              1              1            
      6000   548.42605     -2814.3308      0.76796752     4              1              1            
      6100   525.16391     -2902.5409      0.76796752     4              1              1            
      6200   504.92542     -706.19923      0.76796752     4              1              2            
      6300   531.55271      1217.7795      0.76796752     4              1              2            
      6400   537.29797      264.24006      0.76796752     4              1              2            
      6500   581.8752       2228.1037      0.76796752     4              1              2            
      6600   536.95487     -10318.365      0.76796752     4              2              2            
      6700   498.26961      5005.4587      0.76796752     5              2              2            
      6800   526.00873     -2678.0327      0.76796752     5              2              2            
      6900   542.74619     -1567.8558      0.76796752     5              2              2            
      7000   549.02037      8321.4935      0.76796752     5              2              2            
      7100   542.28295     -1513.6114      0.76796752     5              2              2            
      7200   474.70347      2120.9699      0.76796752     5              2              2            
      7300   506.58637      2588.8837      0.76796752     5              2              2            
      7400   512.45393     -2101371.7      0.76796752     5              2              3            
      7500   546.20285     -2458.3002      0.76796752     5              2              3            
      7600   551.57132      3148.9131      0.76796752     5              2              3            
      7700   544.3684      -775.59686      0.76796752     5              2              3            
      7800   511.32529      2353.0343      0.76796752     5              2              3            
      7900   520.30502      10726.007      0.76796752     5              2              3            
      8000   561.81009      12476.296      0.76796752     5              2              3            
      8100   588.85859      5905.4979      0.76796752     5              2              3            
      8200   490.1071       1132.5027      0.76796752     5              2              3            
      8300   537.65085     -1445.0979      0.76796752     5              2              3            
      8400   523.60343     -589.18012      0.76796752     5              2              3            
      8500   538.90848     -300.32152      0.76796752     5              2              3            
      8600   573.63835      5912.9027      0.76796752     5              2              3            
      8700   557.82593      2585.6634      0.76796752     5              2              3            
      8800   562.5277      -1843272.8      0.76796752     5              2              4            
      8900   564.26894     -1396.8521      0.76796752     5              2              4            
      9000   576.4382       5029.6995      0.76796752     5              2              4            
      9100   514.83258     -935.9015       0.76796752     5              2              4            
      9200   536.33755     -1671.9254      0.76796752     5              2              4            
      9300   494.49553      582.08687      0.76796752     5              2              4            
      9400   532.12156     -6991.3223      0.76796752     6              2              4            
      9500   528.87489      4587.7048      0.76796752     6              2              4            
      9600   555.92299     -3688.5966      0.76796752     6              2              4            
      9700   510.09341      1545.1276      0.76796752     6              2              4            
      9800   505.94984     -4677.2879      0.76796752     6              2              4            
      9900   531.38104      4891.0352      0.76796752     6              2              4            
     10000   517.59995      4299.0553      0.76796752     6              2              4            
Loop time of 29.4182 on 1 procs for 10000 steps with 320 atoms

Performance: 29.370 ns/day, 0.817 hours/ns, 339.926 timesteps/s, 108.776 katom-step/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 10.883     | 10.883     | 10.883     |   0.0 | 36.99
Bond    | 8.0953     | 8.0953     | 8.0953     |   0.0 | 27.52
Kspace  | 2.6136     | 2.6136     | 2.6136     |   0.0 |  8.88
Neigh   | 1.0863     | 1.0863     | 1.0863     |   0.0 |  3.69
Comm    | 0.2095     | 0.2095     | 0.2095     |   0.0 |  0.71
Output  | 0.0019263  | 0.0019263  | 0.0019263  |   0.0 |  0.01
Modify  | 6.4695     | 6.4695     | 6.4695     |   0.0 | 21.99
Other   |            | 0.05924    |            |       |  0.20

Nlocal:            320 ave         320 max         320 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           3425 ave        3425 max        3425 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:          54783 ave       54783 max       54783 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 54783
Ave neighs/atom = 171.19688
Ave special neighs/atom = 10.3375
Neighbor list builds = 460
Dangerous builds = 0

# write_restart restart_longrun nofix
# write_data restart_longrun.data
Total wall time: 0:00:29
